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3BE7
Asym. Unit
Info
Asym.Unit (514 KB)
Biol.Unit 1 (506 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ZN-DEPENDENT ARGININE CARBOXYPEPTIDASE
Authors
:
Y. Patskovsky, U. A. Ramagopal, R. Toro, A. J. Meyer, J. Freeman, M. Iizu K. Bain, L. Rodgers, F. Raushel, J. M. Sauder, S. K. Burley, S. C. Almo, N Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
16 Nov 07 (Deposition) - 27 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Unknown Source, Amidohydrolase, Sargasso Sea, Structural Genomics, Protein Structure Initiative, Psi, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. F. Xiang, Y. Patskovsky, C. Xu, A. J. Meyer, J. M. Sauder, S. K. Burley S. C. Almo, F. M. Raushel
Functional Identification Of Incorrectly Annotated Prolidases From The Amidohydrolase Superfamily Of Enzymes.
Biochemistry V. 48 3730 2009
[
close entry info
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Hetero Components
(3, 26)
Info
All Hetero Components
1a: ARGININE (ARGa)
1b: ARGININE (ARGb)
1c: ARGININE (ARGc)
1d: ARGININE (ARGd)
1e: ARGININE (ARGe)
1f: ARGININE (ARGf)
1g: ARGININE (ARGg)
1h: ARGININE (ARGh)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ARG
8
Mod. Amino Acid
ARGININE
2
GOL
16
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(26, 26)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR F:128 , GLU F:392 , HOH F:556 , HOH F:557 , HOH F:579
BINDING SITE FOR RESIDUE MG F 503
02
AC2
SOFTWARE
THR H:128 , GLU H:392 , HOH H:512 , HOH H:556 , HOH H:577 , HOH H:578
BINDING SITE FOR RESIDUE MG H 502
03
AC3
SOFTWARE
HIS E:142 , GLY E:188 , VAL E:189 , MET E:190 , HIS E:223 , HIS E:225 , HIS E:243 , ASP E:265 , GLU E:289 , VAL E:292 , GLY E:293 , GLN E:296 , ASP E:315 , HOH E:542
BINDING SITE FOR RESIDUE ARG A 501
04
AC4
SOFTWARE
HIS B:142 , GLY B:188 , VAL B:189 , MET B:190 , HIS B:223 , HIS B:225 , HIS B:243 , ASP B:265 , GLU B:289 , VAL B:292 , GLN B:296 , ASP B:315 , HOH B:508
BINDING SITE FOR RESIDUE ARG B 501
05
AC5
SOFTWARE
HOH C:519 , HOH C:536 , HIS D:142 , GLY D:188 , VAL D:189 , MET D:190 , HIS D:223 , HIS D:225 , HIS D:243 , ASP D:265 , VAL D:268 , GLU D:289 , VAL D:292 , GLN D:296 , ASP D:315 , HOH D:540
BINDING SITE FOR RESIDUE ARG C 501
06
AC6
SOFTWARE
HIS C:142 , GLY C:188 , VAL C:189 , MET C:190 , HIS C:223 , HIS C:225 , HIS C:243 , ASP C:265 , GLU C:289 , VAL C:292 , GLN C:296 , ASP C:315 , ILE C:318 , HOH C:518
BINDING SITE FOR RESIDUE ARG D 501
07
AC7
SOFTWARE
HIS F:142 , GLY F:188 , VAL F:189 , MET F:190 , HIS F:223 , HIS F:225 , HIS F:243 , ASP F:265 , VAL F:268 , GLU F:289 , VAL F:292 , GLN F:296 , ASP F:315 , HOH F:551
BINDING SITE FOR RESIDUE ARG E 501
08
AC8
SOFTWARE
HIS G:142 , GLY G:188 , VAL G:189 , MET G:190 , HIS G:223 , HIS G:225 , HIS G:243 , ASP G:265 , GLU G:289 , VAL G:292 , GLN G:296 , ASP G:315 , HOH G:511
BINDING SITE FOR RESIDUE ARG F 501
09
AC9
SOFTWARE
HIS H:142 , GLY H:188 , VAL H:189 , MET H:190 , HIS H:223 , HIS H:225 , HIS H:243 , ASP H:265 , VAL H:268 , GLU H:289 , VAL H:292 , GLN H:296 , ASP H:315 , HOH H:513
BINDING SITE FOR RESIDUE ARG G 501
10
BC1
SOFTWARE
HIS A:142 , GLY A:188 , VAL A:189 , MET A:190 , HIS A:223 , HIS A:225 , HIS A:243 , ASP A:265 , VAL A:268 , GLU A:289 , VAL A:292 , GLN A:296 , ASP A:315 , HOH A:558
BINDING SITE FOR RESIDUE ARG H 501
11
BC2
SOFTWARE
HIS A:64 , GLY A:67 , ASN A:68 , ASP A:69 , ASN A:90 , GLY A:317 , HIS A:321
BINDING SITE FOR RESIDUE GOL A 502
12
BC3
SOFTWARE
SER A:80 , HIS A:81 , ASN A:109 , HOH A:522 , SER B:80 , HIS B:81 , ASN B:109
BINDING SITE FOR RESIDUE GOL A 503
13
BC4
SOFTWARE
ASP B:69 , TRP B:86 , ASN B:90 , LYS B:93 , ASP B:320 , HIS B:321 , HOH B:558
BINDING SITE FOR RESIDUE GOL B 502
14
BC5
SOFTWARE
GLU B:151 , SER C:80 , HIS C:81 , ASN C:109 , SER H:80 , HIS H:81 , ASN H:109
BINDING SITE FOR RESIDUE GOL C 502
15
BC6
SOFTWARE
HIS D:64 , ASP D:69 , ASN D:90 , GLY D:317 , HIS D:321 , HOH D:546
BINDING SITE FOR RESIDUE GOL D 502
16
BC7
SOFTWARE
ASP D:117 , GLU D:120 , ARG D:121 , GLU G:74
BINDING SITE FOR RESIDUE GOL D 503
17
BC8
SOFTWARE
HIS E:64 , GLY E:67 , ASN E:68 , ASP E:69 , ASN E:90 , GLY E:317 , HIS E:321 , HOH E:530
BINDING SITE FOR RESIDUE GOL E 502
18
BC9
SOFTWARE
SER E:80 , HIS E:81 , ASN E:109 , SER F:80 , HIS F:81 , ASN F:109
BINDING SITE FOR RESIDUE GOL E 503
19
CC1
SOFTWARE
GLU F:120 , GLY F:122 , LYS F:391 , GLU F:392
BINDING SITE FOR RESIDUE GOL F 504
20
CC2
SOFTWARE
ASP F:69 , TRP F:86 , ASN F:90 , LYS F:93 , ASP F:320 , HIS F:321
BINDING SITE FOR RESIDUE GOL F 505
21
CC3
SOFTWARE
HIS F:214 , GLY F:217 , ASP F:239
BINDING SITE FOR RESIDUE GOL F 506
22
CC4
SOFTWARE
HIS G:64 , GLY G:67 , ASN G:68 , ASP G:69 , ASN G:90 , GLY G:317 , HIS G:321
BINDING SITE FOR RESIDUE GOL G 502
23
CC5
SOFTWARE
HIS H:214 , GLY H:237 , ASP H:239 , ASN H:258
BINDING SITE FOR RESIDUE GOL H 503
24
CC6
SOFTWARE
ALA H:135 , CYS H:143 , SER H:156 , GLU H:157 , GLY H:158
BINDING SITE FOR RESIDUE GOL H 504
25
CC7
SOFTWARE
ASP H:69 , TRP H:86 , ASN H:90 , LYS H:93 , PHE H:319 , ASP H:320 , HIS H:321
BINDING SITE FOR RESIDUE GOL H 505
26
CC8
SOFTWARE
HIS H:64 , ILE H:65 , GLY H:67 , ASP H:69 , ASN H:90 , HIS H:321
BINDING SITE FOR RESIDUE GOL H 506
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d3be7a1 (A:3-56,A:360-400)
1b: SCOP_d3be7b1 (B:4-56,B:360-398)
1c: SCOP_d3be7c1 (C:5-56,C:360-398)
1d: SCOP_d3be7d1 (D:4-56,D:360-398)
1e: SCOP_d3be7e1 (E:5-56,E:360-398)
1f: SCOP_d3be7f1 (F:4-56,F:360-398)
1g: SCOP_d3be7g1 (G:5-56,G:360-398)
1h: SCOP_d3be7h1 (H:4-56,H:360-398)
2a: SCOP_d3be7a2 (A:57-359)
2b: SCOP_d3be7b2 (B:57-359)
2c: SCOP_d3be7c2 (C:57-359)
2d: SCOP_d3be7d2 (D:57-359)
2e: SCOP_d3be7e2 (E:57-359)
2f: SCOP_d3be7f2 (F:57-359)
2g: SCOP_d3be7g2 (G:57-359)
2h: SCOP_d3be7h2 (H:57-359)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
Zn-dependent arginine carboxypeptidase-like
(4)
Protein domain
:
Zn-dependent arginine carboxypeptidase
(2)
Unidentified organism [TaxId: 32644]
(2)
1a
d3be7a1
A:3-56,A:360-400
1b
d3be7b1
B:4-56,B:360-398
1c
d3be7c1
C:5-56,C:360-398
1d
d3be7d1
D:4-56,D:360-398
1e
d3be7e1
E:5-56,E:360-398
1f
d3be7f1
F:4-56,F:360-398
1g
d3be7g1
G:5-56,G:360-398
1h
d3be7h1
H:4-56,H:360-398
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Zn-dependent arginine carboxypeptidase-like
(4)
Protein domain
:
Zn-dependent arginine carboxypeptidase
(2)
Unidentified organism [TaxId: 32644]
(2)
2a
d3be7a2
A:57-359
2b
d3be7b2
B:57-359
2c
d3be7c2
C:57-359
2d
d3be7d2
D:57-359
2e
d3be7e2
E:57-359
2f
d3be7f2
F:57-359
2g
d3be7g2
G:57-359
2h
d3be7h2
H:57-359
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_3be7A02 (A:59-358)
1b: CATH_3be7B02 (B:59-358)
1c: CATH_3be7C02 (C:59-358)
1d: CATH_3be7D02 (D:59-358)
1e: CATH_3be7E02 (E:59-358)
1f: CATH_3be7F02 (F:59-358)
1g: CATH_3be7G02 (G:59-358)
1h: CATH_3be7H02 (H:59-358)
2a: CATH_3be7A01 (A:3-58,A:359-400)
2b: CATH_3be7B01 (B:4-58,B:359-398)
2c: CATH_3be7D01 (D:4-58,D:359-398)
2d: CATH_3be7F01 (F:4-58,F:359-398)
2e: CATH_3be7H01 (H:4-58,H:359-398)
2f: CATH_3be7C01 (C:5-58,C:359-398)
2g: CATH_3be7E01 (E:5-58,E:359-398)
2h: CATH_3be7G01 (G:5-58,G:359-398)
View:
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Classes
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)
(
)
Architectures
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Metal-dependent hydrolases
(190)
Unidentified. Organism_taxid: 32644.
(2)
1a
3be7A02
A:59-358
1b
3be7B02
B:59-358
1c
3be7C02
C:59-358
1d
3be7D02
D:59-358
1e
3be7E02
E:59-358
1f
3be7F02
F:59-358
1g
3be7G02
G:59-358
1h
3be7H02
H:59-358
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Urease, subunit C; domain 1
(95)
Homologous Superfamily
:
Urease, subunit C, domain 1
(95)
Unidentified. Organism_taxid: 32644.
(2)
2a
3be7A01
A:3-58,A:359-400
2b
3be7B01
B:4-58,B:359-398
2c
3be7D01
D:4-58,D:359-398
2d
3be7F01
F:4-58,F:359-398
2e
3be7H01
H:4-58,H:359-398
2f
3be7C01
C:5-58,C:359-398
2g
3be7E01
E:5-58,E:359-398
2h
3be7G01
G:5-58,G:359-398
[
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]
Pfam Domains
(0, 0)
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Asym.Unit (514 KB)
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